i seriously doubt the twili are the sheikah, they just dont look anything alike, and i doubt being banished to another realm would've changed them so drastically, the sheikah look alot like normal hylians, while the twili look nothing like them, midna's true form is the most human looking, but still not a hylian appearance.
also, the twili's buildings look nothing like that of kakariko village, didnt the sheikah build that village? i would also think they'd have some symbols of the sheikah around the twilight palace, but i dont recall seeing anything of the like...
theres not much similarity between the two other than them both being ancient and secretive, not to me, anyway...